[yocto] do_kernel_configme error when patches create directories

[Jeff Melville]

I'm using a Yocto flow to build for the Zynq with the meta-xilinx with
some customizations:
- I'm using a bbappend to replace the linux-xlnx 3.14 kernel with one
that has had mainline changes from 3.14.17 merged in.
- I added a task between patch and configure for applying the Xenomai
kernel patches and running the Xenomai prepare_kernel script.

All layers are on the dizzy branch. The linux-xlnx recipe inherits
from linux-yocto but obtains the metadeta from an out of tree source
using a SRC_URI append with type=kmeta. This ends up getting copied
into the kernel tree with during the kernel_configme task. This is my
first time working with a kernel recipe in the linux-yocto style so
I'm still coming up to speed a bit.

The problem arises because the Xenomai patch process creates
additional directories in the Linux tree. As part of the
kernel_configme task, the kgit-meta script will attempt to use the
last unversioned directory returned by 'git ls-files -o --directory'
as the metadata directory, which does not work.

Two questions:
1) What is the best short term way for me to work around this?
2) Is there a way to patch the meta directory detection in kgit-meta
to make it more robust against false detections?

Thanks,
Jeff